BACKGROUND Three dimensional computer-assisted reconstruction offers some adventages for analysis and comparison of biological phenomena and anatomical structures. The CDH nitrofen-induced animal model associates multiple anomalies in neural-crest derived tissues. The goal of this study is to analyse by a 3-D reconstruction software the malformations in the extrinsic innervation of the esophagus in this model. METHODS Nine control fetuses from 4 dams and 9 fetuses with CDH from 7 dams were studied. A thoracic block from the larynx to tracheal bifurcation was serially sectioned in the horizontal plane in every embryo. One in every 10 sections was stained with HE. The image was digitalized using biological software (TDR-3dbase). Vagus and recurrent laryngeal nerves, trachea, esophagus and the great vessels were examined. In order to obtain the 3-D reconstructions, 90 to 120 consecutive images were used. RESULTS In comparison with controls there were striking abnormalities of these nerves in fetuses with CDH: 1) Absence of the left (2/9) or right (2/9) vagus nerves. 2) Absence of the left (3/9) or right (3/9) recurrent laryngeal nerves. 3) Marked hypoplasia of the trunk of the vagus (2/9). 4) Deviations of their normal course and change of normal anatomical relationships into the mediastinum (2/9). CONCLUSIONS To fullfill our goals 3-D reconstructions allow a detailed analysis and provide a precise insight into the real anatomy. Rat fetuses with CDH have anomalies of the vagus and recurrent laryngeal nerves that support the concept of a neural crest involvement in the origin of this malformation. These observations may explain esophageal motility disorders in CDH.